Unable to run RSEM because of error rsem-parse-alignments : No such file or directory

Question

[mohammedtoufiq91]

Hi,

I downloaded the RSEM software package for estimating gene and isoform expression levels from RNA-Seq data, then compiled RSEM using make in the same directory, throws many errors and warnings:

In file included from simulation.cpp:22:
In file included from ./SingleModel.h:16:
In file included from ./Orientation.h:8:
In file included from ./simul.h:6:
In file included from ./boost/random.hpp:52:
In file included from ./boost/random/generate_canonical.hpp:22:
In file included from ./boost/math/special_functions.hpp:15:
In file included from ./boost/math/special_functions/airy.hpp:10:
In file included from ./boost/math/special_functions/bessel.hpp:21:
In file included from ./boost/math/special_functions/detail/bessel_jy_zero.hpp:25:
./boost/math/special_functions/detail/airy_ai_bi_zero.hpp:91:24: error: no template named 'tuple' in namespace 'boost::math'
          boost::math::tuple<T, T> operator()(const T& x) const
          ~~~~~~~~~~~~~^
./boost/math/special_functions/detail/airy_ai_bi_zero.hpp:94:33: error: no member named 'make_tuple' in namespace 'boost::math'
            return boost::math::make_tuple(
                   ~~~~~~~~~~~~~^
./boost/math/special_functions/detail/airy_ai_bi_zero.hpp:142:24: error: no template named 'tuple' in namespace 'boost::math'
          boost::math::tuple<T, T> operator()(const T& x) const
          ~~~~~~~~~~~~~^
./boost/math/special_functions/detail/airy_ai_bi_zero.hpp:145:33: error: no member named 'make_tuple' in namespace 'boost::math'
            return boost::math::make_tuple(
                   ~~~~~~~~~~~~~^
In file included from simulation.cpp:22:
In file included from ./SingleModel.h:16:
In file included from ./Orientation.h:8:
In file included from ./simul.h:6:
In file included from ./boost/random.hpp:52:
In file included from ./boost/random/generate_canonical.hpp:22:
In file included from ./boost/math/special_functions.hpp:15:
In file included from ./boost/math/special_functions/airy.hpp:10:
In file included from ./boost/math/special_functions/bessel.hpp:21:
./boost/math/special_functions/detail/bessel_jy_zero.hpp:62:22: error: no template named 'tuple' in namespace 'boost::math'
        boost::math::tuple<T, T> operator()(const T& z) const
        ~~~~~~~~~~~~~^
./boost/math/special_functions/detail/bessel_jy_zero.hpp:78:31: error: no member named 'tuple' in namespace 'boost::math'
          return boost::math::tuple<T, T>(the_function, its_derivative);
                 ~~~~~~~~~~~~~^
./boost/math/special_functions/detail/bessel_jy_zero.hpp:78:37: error: 'T' does not refer to a value
          return boost::math::tuple<T, T>(the_function, its_derivative);
                                    ^
./boost/math/special_functions/detail/bessel_jy_zero.hpp:56:25: note: declared here
      template<typename T>
                        ^
./boost/math/special_functions/detail/bessel_jy_zero.hpp:211:24: error: no template named 'tuple' in namespace 'boost::math'
          boost::math::tuple<T, T> operator()(const T& x) const
          ~~~~~~~~~~~~~^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
6 warnings and 20 errors generated.
make: *** [simulation.o] Error 1

Then, tried running RSEM

./rsem-calculate-expression --bowtie2 --bowtie2-path /Users/Documents/Bioinformatics_tools/Bowtie2/bowtie2-2.5.0-macos-x86_64  -p 8  --output-genome-bam --paired-end /Users/Documents/Bioinformatics_tools/SRA/fastq_dir/SRR1039508_1.fastq /Users/Documents/Bioinformatics_tools/SRA/fastq_dir/SRR1039508_2.fastq /Users/Documents/Bioinformatics_tools/Bowtie2/index/GRCh38_noalt_as/GRCh38_noalt_as  hg_paired_end_quals

but it shows the below error, I guess this is searching for this file, but this not generated after compiling using make command?

rsem-parse-alignments : No such file or directory!

I tried to trouble shoot the issue using this link but unsuccessful rsem-calculate-expression error

Best Regards, Toufiq

[Pierre Lindenbaum]

error: no template named 'tuple' in namespace 'boost::math'

same (unsolved) error on github : https://github.com/deweylab/RSEM/issues/189

[mohammedtoufiq91]

Pierre Lindenbaum, thank you for the response. Does posting this question on stackoverflow should help me resolve this? This tool is very important for my analysis.

[Pierre Lindenbaum]

Well I would say that a compilation flag is missing in the Makefile, or you're using an old version of gcc, but you can always post to SO.

[mohammedtoufiq91]

Pierre Lindenbaum thank you very much.